GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12660 in Pseudomonas stutzeri RCH2

Align D-lactate transporter, permease component 2 (characterized)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components

Query= reanno::Phaeo:GFF1250
         (340 letters)



>FitnessBrowser__psRCH2:GFF3786
          Length = 295

 Score =  176 bits (447), Expect = 5e-49
 Identities = 113/335 (33%), Positives = 166/335 (49%), Gaps = 51/335 (15%)

Query: 1   MDAILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLS 60
           + A L Q+L GL  GS YA+++LGL +IFG L ++NFAHGA +MIGAF    +   L + 
Sbjct: 9   IQAFLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYLLLATLGIG 68

Query: 61  FETVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGV-GYVME 119
           +                                    W      L   PI++G+   V+E
Sbjct: 69  Y------------------------------------WPA----LILAPIIVGLCSAVIE 88

Query: 120 RGLIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMD 179
           R  +   Y   H   +L TFGLA+ L+   +YFYG++      P  L G  NLG +    
Sbjct: 89  RLALSRLYNLDHLYSLLFTFGLALALEGAFRYFYGSSGQPYAVPKELAGGYNLGFMF--- 145

Query: 180 IVYPVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFG 239
              P +R      ++VI    +  ++ T  G  +RA   +   V   GIN+    T  +G
Sbjct: 146 --LPKYRAWVVLASLVICIASWLLIEKTKLGAYLRAATENPTLVRTFGINVPLLLTFTYG 203

Query: 240 IAAAVAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFA 299
           + AA+AGLAG++  PI   +  MG + +++ F VVVVGGMGS+ GA++ G++LG+LE   
Sbjct: 204 MGAALAGLAGMLAAPIYQVSPLMGSNLIIVVFAVVVVGGMGSILGAIITGYMLGILEGLT 263

Query: 300 SMNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGR 334
                K   P    I+I+V+  I+LL RP GLMGR
Sbjct: 264 -----KVFYPEASNIVIFVIMAIVLLVRPAGLMGR 293


Lambda     K      H
   0.329    0.147    0.439 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 272
Number of extensions: 18
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 340
Length of database: 295
Length adjustment: 27
Effective length of query: 313
Effective length of database: 268
Effective search space:    83884
Effective search space used:    83884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory